Vigilante (Japan, Rev D) - this is what the screen looks like from a fresh boot of the MiSTer connected to a CRT:
Notice how the screen is as it should be, according to my custom vertical and horizontal settings in the OSD.
If I turn the CRT off, then back on, this is what the screen looks like:
Note the black gap at the bottom of the screen (where I placed the red rectangle). The screen has shifted upwards.
I was not able to replicate this behaviour with other cores, although I didn't test many. For this reason, I am going to guess that this may be an issue with the core, rather than my CRT. I note that adjusting the offsets after turning the CRT off then on does not allow me to get back to the position seen in the first screen shot. Reloading the core also does not fix the issue. The only way to fix is to either switch the MiSTer off then back on again or switch to another core then back to the Vigilante core.